Hi,
I am using below command to extract bacterial taxonomy by using gene id name in txt file, one gene id PER LINE, but it is showing some error, please advise me how I can resolve it? there are around 60000 gene id in arms.ID.txt file.
I need taxonomy in this format:
AM774418.1 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium Halobacterium salinarum R1
LOPV01000533.1 Archaea; Euryarchaeota; Halobacteria; Haloferacales; Haloferacaceae; Haloferax Haloferax sp. SB29
CP003125.1 Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus; Geobacillus thermoleovorans group Geobacillus thermoleovorans CCB_US3_UF5
BAWP01000033.1 Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Parageobacillus Parageobacillus thermoglucosidasius NBRC 107763
efetch -db nuccore -format gbc -id arsM.ID.txt|xtract -pattern INSDSeq -element INSDSeq_accession-version INSDSeq_taxonomy INSDSeq_organism >arsm.taxonomy
Error:
501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=arsM.ID.txt&rettype=gbc&retmode=xml&edirect_os=linux&edirect=11.7&tool=edirect&email=3052771@login4.pri.kelvin2.alces.network'
Result of do_post http request is
$VAR1 = bless( {
'_content' => 'LWP will support https URLs if the LWP::Protocol::https module
is installed.
',
'_msg' => 'Protocol scheme \'https\' is not supported (LWP::Protocol::https not installed)',
'_headers' => bless( {
'content-type' => 'text/plain',
'client-warning' => 'Internal response',
'::std_case' => {
'client-date' => 'Client-Date',
'client-warning' => 'Client-Warning'
},
'client-date' => 'Mon, 22 Jul 2019 14:38:30 GMT'
}, 'HTTP::Headers' ),
'_rc' => 501,
'_request' => bless( {
'_content' => 'db=nuccore&id=arsM.ID.txt&rettype=gbc&retmode=xml&edirect_os=linux&edirect=11.7&tool=edirect&email=3052771@login4.pri.kelvin2.alces.network',
'_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
'_headers' => bless( {
'content-type' => 'application/x-www-form-urlencoded',
'user-agent' => 'libwww-perl/6.39'
}, 'HTTP::Headers' ),
'_method' => 'POST'
}, 'HTTP::Request' )
}, 'HTTP::Response' );
vi arsM.ID.txt
AAAK03000116.1
AAAL02000001.1
AACD01000079.1
AACS02000002.1
AADV02000002.1
error is
answer is:
https://stackoverflow.com/questions/21123620
The user should first do a fresh reinstall of EDirect, most importantly running the "./edirect/setup.sh" command at the end of the installation instructions, in order to get all of the Perl modules properly loaded.
Then he should execute the following commands:
This method makes the most efficient use of the server. The only potential issue is that the result will not be sorted in the original order:
and the -sort argument is not supported by the underlying epost.fcgi server. If he really needs it in the original order, then using a for loop is necessary, though time-consuming and inefficient.
Thanks, as I was getting error on HPC server so I installed EDirect on iMac from this link: E-Direct: https://www.ncbi.nlm.nih.gov/books/NBK179288/
and I tried below command to extract taxonomy and got some error:
But I will try with API_KEY bash script as you shared if it can work.
Thanks
I did used this script but it is showing some error:
script:
Did you follow the install instructions fully? Especially this part
./edirect/setup.sh
.Can you use my script below and see what it produces?
Unfortunately this user is using a cluster and is not able to do anything with installed software.
Have you signed up for
NCBI_API_KEY
and are using it? If you are using a long list of queries NCBI may be limiting number of your queries.thanks, I put API_key, at the end of the command: but still showing same error:
I am working on HPC, What module should I load to resolve this issue?
Thanks bioinfonext
That is the wrong position to put the API key. I suggest that you export it as a variable in your shell session (or permanently in your .bashrc or .profile). Do
export NCBI_API_KEY=your_key
and then run the command only containing output file nameup to > arsm.taxonomy
.I assume the error about
https
is not critical since you have usedncbi eutils
on this machine successfully before?thanks, let me try to run this as a bash script.
bioinfonext
Hi,
I am trying to run above command with this scrip but it is not running: could you please advise if there is any error in the script:
I see you guys tracking the API key, but from my own experience I can share that the LWP issue is critical, see Pierre's first comment. On your HPC, you might need to load some additional Perl module containing LWP
Presumably
eutils
has worked on this cluster based on past questions posted by this poster. We are going with that premise.fair enough, taking the full user profile into account is first class service - kudos!